In 2006 Moorhouse's first solo book, Killing Hitler, was published, which has since appeared in numerous other languages, including German, Spanish, Chinese, Italian and Japanese. In a CNN news report of 3 September 2011, Killing Hitler was shown on Al-Saadi Gaddafi's desk after he had fled his office in the wake of the collapse of the Gaddafi regime in Libya. Reporter Nic Robertson suggested that Saadi Gaddafi had been reading the book prior to his flight.[3]

His next book, Berlin at War, is a social history of Berlin during World War II, which was published in the summer of 2010. Writing in the Financial Times, Andrew Roberts said of it that: "Few books on the war genuinely increase the sum of our collective knowledge of this exhaustively covered period, but this one does."[4] "Berlin at War" was listed amongst the books of the year for 2010 by the Daily Telegraph, American Spectator magazine and others, and was shortlisted for the Hessell-Tiltman Prize for history.[5]

In 2014 his The Devils' Alliance: Hitler's Pact with Stalin, 1939-1941 was published. Whilst praising the book for its "masterly" account of the signing of the Molotov–Ribbentrop Pact, historian Richard J. Evans took exception to the book's "unbalanced treatment" of the crimes of the Soviets over those of the Nazis, saying that "for all its virtues this is a deeply problematic book".[6] Other reviewers of the book were more positive – the Wall Street Journal described it as "superb"[7] and the Daily Telegraph listed it among its Books of the Year for 2014.[8]